rs249153
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000552205.6(NDUFA12):n.258-2350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,116 control chromosomes in the GnomAD database, including 4,286 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.23 ( 4286 hom., cov: 32)
Consequence
NDUFA12
ENST00000552205.6 intron
ENST00000552205.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.48
Publications
12 publications found
Genes affected
NDUFA12 (HGNC:23987): (NADH:ubiquinone oxidoreductase subunit A12) This gene encodes a protein which is part of mitochondrial complex 1, part of the oxidative phosphorylation system in mitochondria. Complex 1 transfers electrons to ubiquinone from NADH which establishes a proton gradient for the generation of ATP. Mutations in this gene are associated with Leigh syndrome due to mitochondrial complex 1 deficiency. Pseudogenes of this gene are located on chromosomes 5 and 13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2012]
NDUFA12 Gene-Disease associations (from GenCC):
- mitochondrial complex I deficiency, nuclear type 23Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- Leigh syndrome with leukodystrophyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Leigh syndromeInheritance: AR Classification: LIMITED Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Frequencies
GnomAD3 genomes AF: 0.227 AC: 34447AN: 151994Hom.: 4278 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
34447
AN:
151994
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.227 AC: 34467AN: 152116Hom.: 4286 Cov.: 32 AF XY: 0.223 AC XY: 16584AN XY: 74380 show subpopulations
GnomAD4 genome
AF:
AC:
34467
AN:
152116
Hom.:
Cov.:
32
AF XY:
AC XY:
16584
AN XY:
74380
show subpopulations
African (AFR)
AF:
AC:
13303
AN:
41490
American (AMR)
AF:
AC:
2758
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
643
AN:
3470
East Asian (EAS)
AF:
AC:
456
AN:
5184
South Asian (SAS)
AF:
AC:
613
AN:
4824
European-Finnish (FIN)
AF:
AC:
1673
AN:
10572
Middle Eastern (MID)
AF:
AC:
47
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14288
AN:
67976
Other (OTH)
AF:
AC:
468
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1342
2685
4027
5370
6712
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
352
704
1056
1408
1760
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
392
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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